Mercurial > repos > cropgeeks > ukseed

changeset 26:d1d232d4cb2f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author cropgeeks
date Fri, 20 Apr 2018 14:44:25 -0400
parents ae6b94d10bff
children 558a46a635a9
files dartseq_seeduk_2b.R ukseed_stage2.xml
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/dartseq_seeduk_2b.R	Fri Apr 20 12:42:06 2018 -0400
+++ b/dartseq_seeduk_2b.R	Fri Apr 20 14:44:25 2018 -0400
@@ -4,7 +4,7 @@
 library("labdsv")
 
 data <- read.table("plink.raw",header=T)
-distances <- Dist(data[,7:dim(data)[2]], method = "euclidean", nbproc = 144)
+distances <- Dist(data[,7:dim(data)[2]], method = "euclidean", nbproc = as.integer(args[2]))
 pco_results <- pco(distances,k=10)
 #Variance explained by first three PCOs
 pco_results$eig[1]/sum(pco_results$eig[pco_results$eig>0])
--- a/ukseed_stage2.xml	Fri Apr 20 12:42:06 2018 -0400
+++ b/ukseed_stage2.xml	Fri Apr 20 14:44:25 2018 -0400
@@ -14,7 +14,7 @@
 		&&		
 		plink --bfile test --recode A 
 		&&		
-		Rscript --vanilla $__tool_directory__/dartseq_seeduk_2b.R $output		
+		Rscript --vanilla $__tool_directory__/dartseq_seeduk_2b.R $output \${GALAXY_SLOTS:-1} 	
     ]]></command>
 	
     <inputs>